Solution structure of dengue virus capsid protein reveals another fold

Abstract

Dengue virus is responsible for Ϸ50 -100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C protein. The structure provides, to our knowledge, the first 3D picture of a flavivirus C protein and identifies a fold that includes a large dimerization surface contributed by two pairs of helices, one of which has characteristics of a coiled-coil. NMR structure determination involved a secondary structure sorting approach to facilitate assignment of the intersubunit nuclear Overhauser effect interactions. The dimer of dengue C protein has an unusually high net charge, and the structure reveals an asymmetric distribution of basic residues over the surface of the protein. Nearly half of the basic residues lie along one face of the dimer. In contrast, the conserved hydrophobic region forms an extensive apolar surface at a dimer interface on the opposite side of the molecule. We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results.D engue virus, a member of the flavivirus genus of enveloped RNA viruses, is one of the most significant mosquito-borne viral pathogens, given the impact of the recent resurgence of dengue fever and dengue hemorrhagic fever (1). Other members of the flavivirus genus are also important human pathogens and include such viruses as yellow fever, West Nile virus, and Japanese encephalitis (2). The structure of dengue virus was recently described by using cryo-electron microscopy, which permitted visualization of certain viral protein components (3). The organization of the major envelope glycoprotein (E) in the virion was obtained by fitting the atomic structure of the ectodomain from the related tick-borne encephalitis (TBE) E protein into the outermost layer of density (4). Density internal to the E ectodomain demonstrated a host-derived lipid bilayer with transmembrane helices from E and the small structural protein M (5). Interior to the bilayer is the nucleocapsid core that comprises multiple copies of the capsid, or core, protein (C) and a single 10.7-kb genome RNA. Surprisingly, the organization of the C protein within the nucleocapsid core layer is not discernable. The lack of strong density for C may suggest a rather unique architecture of the flavivirus nucleocapsid core that is distinct from the structural organization of morphologically related viruses such as alphaviruses, a genus in the Togaviridae family of mosquito-borne viruses.The dengue C protein is essential in virus assembly to ensure specific encapsidation of the viral genome. The critical role of C is evident from the existence of subviral particles that are released from infected cells but lack C protein and genome RNA (6). The me...

Nucleic acid delivery by cell penetrating peptides derived from dengue virus capsid protein: design and mechanism of action

“…However, application of these proteins as drug delivery systems is limited by their size. For instance, dengue virus capsid (DENV C) protein is a 100-amino acid protein occurring as a homodimer [16,17] (Fig. 1A).…”

“…In this work, two such peptides, pepR and pepM (Fig. 1B,C), have been derived from two DENV C protein regions conserved among Flaviviridae family members [16,17]: a highly cationic amino acid residue sequence and a hydrophobic one, putatively assigned as RNA-binding and membrane-binding sequences (RBS and MBS respectively; Fig. 1).…”

Escherichia coli Cell Surface Perturbation and Disruption Induced by Antimicrobial Peptides BP100 and pepR

“…A strong selectivity toward anionic bacterial membrane models was detected for BP100, with a strong correlation between the closely coupled processes of charge neutralization, permeabilization, and translocation being identified. The second peptide, pepR (LKRWGTIKKSKAINVLRGFRKEIGRMLNILNRRRR), is derived from the putative RNA-binding domain of the dengue virus capsid protein (15). The structural features of this peptide as observed in the capsid protein (i.e.…”

Papel de las células dendríticas en la infección por el virus dengue: blancos de replicación y respuesta inmune

“…Pertenece a la familia Flaviviridae y es un virus envuelto con genoma ARN monocatenario de polaridad positiva [ssRNA(+)] que codifica para tres proteínas estructurales (C, prM, E) y siete no estructurales (NS1, NS2A, NS2B, NS3, NS4A, NS4B y NS5) (Figura 1), involucradas en la replicación del ARN, el ensamblaje del virus y la modulación de la respuesta inmune de la célula hospedera [7][8][9][10] (Tabla 1). Múltiples monómeros de la proteína C encapsidan el ARN viral para formar la nucleocápside 11,12 , la que está rodeada por una bicapa lipídica de origen celular donde se encuentran ancladas las proteínas M (matriz) y E (envoltura) 13 . La proteína E es de especial importancia para el reconocimiento y unión a los receptores que median la entrada del virus a la célula blanco 4 , por endocitosis mediada por receptor; así inicia su ciclo de replicación.…”